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Toward practical transparent verifiable and long-term reproducible research using Guix
16 references·2 citing·39 second hop
Toward practical transparent verifiable and long-term reproducible research using Guix (2022)Toward practical transparent verifiable a…The fundamental principles of reproducibility (2021)The fundamental principles of…Ten simple rules on writing clean and reliable open-source scientific software (2021)Ten simple rules on writing c…Investigating the replicability of preclinical cancer biology (2021)Investigating the replicabili…Challenges for assessing replicability in preclinical cancer biology (2021)Challenges for assessing repl…Assessment of transparency indicators across the biomedical literature: How open is open? (2021)Assessment of transparency in…The Essential Toolbox of Data Science: Python, R, Git, and Docker (2020)The Essential Toolbox of Data…Ten simple rules for writing Dockerfiles for reproducible data science (2020)Ten simple rules for writing …Challenge to scientists: does your ten-year-old code still run? (2020)Challenge to scientists: does…Reproducibility vs. Replicability: A Brief History of a Confused Terminology (2018)Reproducibility vs. Replicabi…Software simplified (2017)Software simplifiedSingularity: Scientific containers for mobility of compute (2017)Singularity: Scientific conta…Practical Computational Reproducibility in the Life Sciences (2017)Practical Computational Repro…The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)The Galaxy platform for acces…How open science helps researchers succeed (2016)How open science helps resear…1,500 scientists lift the lid on reproducibility (2016)1,500 scientists lift the lid…Web‐Based Analysis and Publication of Flow Cytometry Experiments (2010)Web‐Based Analysis and Public…Source Code Archiving to the Rescue of Reproducible Deployment (2024)Source Code Archiving to the …Automatic Reproduction of Workflows in the Snakemake Workflow Catalog and nf-core Registries (2023)Automatic Reproduction of Wor…flowCore: a Bioconductor package for high throughput flow cytometry (2009)The Stanford Data Miner: a novel approach for integrating and exploring heterogeneous immunological data (2012)GenePattern flow cytometry suite (2013)OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis (2014)Galaxy: A platform for interactive large-scale genome analysis (2005)Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018)Free online availability substantially increases a paper's impact (2001)Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python (2011)Who's Afraid of Peer Review? (2013)Open Science now: A systematic literature review for an integrated definition (2018)Open science challenges, benefits and tips in early career and beyond (2019)Web of Science (WoS) and Scopus: The Titans of Bibliographic Information in Today’s Academic World (2021)Reproducible Research in Computational Science (2011)Journal of Computational Neuroscience (2013)What does research reproducibility mean? (2016)Open science, reproducibility, and transparency in ecology (2018)Reproducibility in machine learning for health research: Still a ways to go (2021)Jupyter Notebooks – a publishing format for reproducible computational workflows (2016)Streamlining data-intensive biology with workflow systems (2021)The five pillars of computational reproducibility: bioinformatics and beyond (2023)Empowering bioinformatics communities with Nextflow and nf-core (2025)Why Most Published Research Findings Are False (2005)The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement: Guidelines for Reporting Observational Studies (2007)The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement: Guidelines for Reporting Observational Studies (2007)Biosecurity in an age of open science (2022)Is the future of peer review automated? (2022)Quantitative research assessment: using metrics against gamed metrics (2023)The file drawer problem and tolerance for null results. (1979)The case for motivated reasoning. (1990)Replication concerns in sports and exercise science: a narrative review of selected methodological issues in the field (2022)Reproducibility in Neuroimaging Analysis: Challenges and Solutions (2022)Estimating the reproducibility of psychological science (2015)Build up big-team science (2022)The replication crisis has led to positive structural, procedural, and community changes (2023)A manifesto for reproducible science (2017)The nf-core framework for community-curated bioinformatics pipelines (2020)Sustainable data analysis with Snakemake (2021)
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References

  • 20161,500 scientists lift the lid on reproducibility4,200 cited
  • 2017Singularity: Scientific containers for mobility of compute2,734 cited
  • 2016The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update2,149 cited
  • 2016How open science helps researchers succeed790 cited
  • 2010Web‐Based Analysis and Publication of Flow Cytometry Experiments511 cited
  • 2018Reproducibility vs. Replicability: A Brief History of a Confused Terminology426 cited
  • 2021Investigating the replicability of preclinical cancer biology419 cited
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  • 2017Practical Computational Reproducibility in the Life Sciences158 cited
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  • 2017Software simplified

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25 cited
  • 2020The Essential Toolbox of Data Science: Python, R, Git, and Docker21 cited
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    • 2023Automatic Reproduction of Workflows in the Snakemake Workflow Catalog and nf-core Registries11 cited
    • 2024Source Code Archiving to the Rescue of Reproducible Deployment8 cited